期刊文献

RGD v2.0: a major update of the ruminant functional and evolutionary genomics database 收藏

RGD v2.0：反刍动物功能和进化基因组学数据库的重大更新

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作者

Weiwei Fu [1];Rui Wang [1];Hojjat Asadollahpour Nanaei [1];Jinxin Wang [1];Dexiang Hu [1];Yu Jiang [1]

作者单位

[1]Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China Center for Ruminant Genetics and Evolution, Northwest A&F University, Yangling 712100, China

关键词

phenotype;breeding;cattle;genes;genome;genomics;ruminants;sheep;synteny;tau proteins;farm animals;galveston orientation and amnesia test;basic local alignment search tool;datasets;epigenomics;rna-seq

关键词译文

表型;养殖;基因;基因组;反刍动物;羊;同步; Tau蛋白;农场动物;加尔维斯顿定位和遗忘测试;基本的本地对准搜索工具;数据集;表观组织; rna-seq

发布日期

13 October 2021

页码

D1091-D1099

DOI

10.1093/nar/gkab887

来源信息

Nucleic Acids Research ISSN：0305-1048, 2022年, 50卷, D1期, D1091-D1099页

摘要

Ruminant Genome Database (RGD; http://animal.nwsuaf.edu.cn/RGD) provides visualization and analysis tools for ruminant comparative genomics and functional annotations. As more high-quality ruminant genome assemblies have become available, we have redesigned the user interface, integrated and expanded multi-omics data, and developed novel features to improve the database. The new version, RGD v2.0, houses 78 ruminant genomes; 110-species synteny alignments for major livestock (including cattle, sheep, goat) and wild ungulates; 21 012 orthologous gene clusters with Gene Ontology and pathway annotation; ∼8 600 000 conserved elements; and ∼1 000 000 cis-regulatory elements by utilizing 1053 epigenomic data sets. The transcriptome data in RGD v2.0 has nearly doubled, currently with 1936 RNA-seq data sets, and 155 174 phenotypic data sets have been newly added. New and updated features include: (i) The UCSC Genome Browser, BLAT, BLAST and Table Browser tools were updated for six available ruminant livestock species. (ii) The LiftOver tool was newly introduced into our browser to allow coordinate conversion between different ruminant assemblies. And (iii) tissue specificity index, tau, was calculated to facilitate batch screening of specifically expressed genes. The enhanced genome annotations and improved functionality in RGD v2.0 will be useful for study of genome evolution, environmental adaption, livestock breeding and biomedicine.

摘要译文

反刍动物基因组数据库（RGD; http://animal.nwsuaf.edu.cn/rgd）为反刍动物比较基因组学和功能注释提供可视化和分析工具。随着更高质量的反刍动物基因组组件已有可用，我们已重新设计用户界面，集成和扩展的多OMICS数据，并开发了新颖的功能以改进数据库。新版本RGD v2.0，拥有78个反刍动物基因组; 110种Synteny用于主要牲畜（包括牛，绵羊，山羊）和野生非粗物体的对齐; 21 012与基因本体和途径注释的局部基因簇; 〜8 600 000保守元素;通过利用1053个表观组织数据集和~1 000 000平顺性元素。 RGD V2.0中的转录组数据几乎翻了一番，目前使用1936 RNA-SEQ数据集，并新增155个174个表型数据集。新的和更新功能包括：（i）UCSC基因组浏览器，Blat，Blast和表浏览器工具已更新为六种可用反刍动物牲畜物种。（ii）新推出的升降工具被新引入我们的浏览器，以允许在不同反刍动物组件之间坐标转换。（III）组织特异性指数TAU，以促进特异性表达基因的批量筛查。 RGD v2.0中增强的基因组注释和改善的功能对于基因组演化，环境适应，牲畜育种和生物医学研究是有用的。

Weiwei Fu [1];Rui Wang [1];Hojjat Asadollahpour Nanaei [1];Jinxin Wang [1];Dexiang Hu [1];Yu Jiang [1]. RGD v2.0: a major update of the ruminant functional and evolutionary genomics database[J]. Nucleic Acids Research, 2022,50(D1): D1091-D1099